Surely just a towering story's base

Because of the isolation inherent in Pandora's Tower (you, your cursed love interest and some kind of merchant witch are the only ones hanging around an old, abandoned frontier base), its story is neatly two-pronged. One of these prongs is the story of the world at large, the war between Elyria and Athos, and the creation of the towers. The other is the story of Elena and Aeron - how they met, what their relationship was like before Elena was cursed, and what their relationship is becoming as Aeron strives to gather the flesh of each of the thirteen towers' masters in time.

Other games run simultaneous plots on multiple levels, but in Pandora's Tower the two plots are much more distinct from each other. That's not to say they aren't intertwined. Elena and Aeron's relationship is a story of star-crossed lovers from nations at war, but at the same time, their relationship is an example of the two nations co-existing. It's a microcosm of the world and its goings on. Elyria is merely suspicious of Athos at this point in the game, but there's trouble brewing there, and likewise, as Elena becomes lonelier and lonelier, she's likely to change as well. Though I doubt that she would ever become hostile towards Aeron. 

Still, two plots so straightforward in their motion could do with some shaking up - there's no doubt the game's developer Ganbarion knows this and put something disruptive to both plots down the line somewhere. I'd expect nothing less from a company that's worked on anime projects in the past.